Arsenal will limp back into the Champions League this week a side wounded. Any momentum they had hoped to carry into Tuesday's daunting tie against Bayern Munich drained away here with the hosts jettisoned unceremoniously from the FA Cup by Blackburn, a side whose primary aim this term is a mere place in the Championship play-offs. This campaign had already been traumatic at times but this loss, so untimely as it was, felt like a new nadir.

Never before had Arsène Wenger suffered defeat at home to lower-league opposition over his 17-year tenure in England. Indeed, his side had never previously succumbed at all in this competition to a team from outside the Premier League. Yet, when Wojciech Szczesny pushed away Martin Olsson's shot 18 minutes from time and the loose ball was scuffed down by Colin Kazim-Richards, an Arsenal supporter no less, to loop into a gaping net that record was in tatters. This club's hopes of winning a first trophy in eight years now hinge entirely upon Europe. That prospect, just like this defeat, feels utterly unlikely.

This was the second upset endured this term, following Bradford's success on penalties in the League Cup, to leave Wenger ashen-faced through his post-match assessments. "We were not good enough to win the game today, simple as that," he offered through a monotone. "We lacked ruthlessness in front of goal, didn't make enough of our offensive corners, and we were vulnerable to one mistake."

Had his team selection been a risk? "No. We had 11 international players on the pitch at the start of the game, and when we made the changes it was still 0-0." Is this now threatening to be his worst season to date at the club? "The season is not over. For some people it may be, but not for me." Yet it will take an almighty injection of confidence in the first leg against Bayern to lift this club, particularly given Arsenal's wretched record away from home in European knockout ties over the past five years. The hope was that this game might provide a fillip ahead of a crunch occasion, though it ended with grumbling discontent in the stands transformed into livid complaints.

The management predictably pointed to the possession statistics, the corner count or even the attempts made at goal – "We had 70% of the ball, 16 shots at goal, and they had one on goal," Wenger said – but so much of this failure was of Arsenal's own making. Rovers were hardly tidy but too often home players made progress down the flanks then could only cross in hope towards a lonely Olivier Giroud, the Frenchman forever lost in the clutter of visiting defenders. Scott Dann and Grant Hanley were strong and resolute, barking instructions at colleagues throughout, while Jake Kean enjoyed an inspired afternoon. There were first-half saves from Abou Diaby and Thomas Vermaelen, and a late claim from Theo Walcott's header.

Yet, aside from Tomas Rosicky belting an attempt from distance on to the bar, that was as fraught as this felt. The massed ranks of visiting players in the six-yard box could cope while Arsenal's presence in the penalty area was so thin. Michael Appleton's tactics had allowed for crosses raining down upon his back line, but there were man-markers in there to deal with that threat. More worrying were balls threaded through Rovers' rearguard, yet only once were they sprung and that opportunity, thankfully for Blackburn, fell to Gervinho. Rosicky's first-time pass inside Hanley was delightful, the Ivorian galloping through to collect. But, as Kean tumbled to his left, the forward's finish drifted wide of the far post and the hosts' best chance had been fluffed.

Wenger eventually flung on the cavalry, as he had against Brighton in the previous round, but Arsenal were still adjusting when Hanley's punt and Jordan Rhodes's flick-on allowed Martin Olsson his sight of goal. Within seconds, Kazim-Richards was celebrating the contest's only goal and Appleton, a manager who has endured so much over a fledgling career, could celebrate his finest achievement yet. Rovers had been humiliated 7-1 in the Premier League here last season but, under their fifth manager of the current campaign, they have unearthed resilience that is threatening progress.

"Fundamentally, you don't win games of football without being organised," Appleton said. "That's the first thing we've done. We're hard to beat, and we have a bit of quality as well." Their solidity was admirable here to ensure the 37-year-old, who has already been eliminated from this competition with Portsmouth this term and drew a third-round tie at Fulham while with Blackpool, has a quarter-final ahead. He joked about having to "bring his players down" ahead of Tuesday's game with Hull. Wenger must somehow achieve precisely the opposite as Bayern steamroller into town.